HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.

Log message:
htslib: updated to 1.9
1.9:
If ./configure fails, make will stop working until either configure is re-run \
successfully, or make distclean is used. This makes configuration failures more \
obvious.
The default SAM version has been changed to 1.6. This is in line with the latest \
version specification and indicates that HTSlib supports the CG tag used to \
store long CIGAR data in BAM format.
bgzip integrity check option '--test'
Faidx can now index fastq files as well as fasta. The fastq index adds an extra \
column to the .fai index which gives the offset to the quality values. New \
interfaces have been added to htslib/faidx.h to read the fastq index and \
retrieve the quality values. It is possible to open a fastq index as if fasta \
(only sequences will be returned), but not the other way round.
New API interfaces to add or update integer, float and array aux tags.
Add level=<number> option to hts_set_opt() to allow the compression level \
to be set. Setting level=0 enables uncompressed output.
Improved bgzip error reporting.
Better error reporting when CRAM reference files can't be opened.
Fixes to make tests work properly on Windows/MinGW - mainly to handle line \
ending differences.
Efficiency improvements:
Small speed-up for CRAM indexing.
Reduce the number of unnecessary wake-ups in the thread pool.
Avoid some memory copies when writing data, notably for uncompressed BGZF output.
Bug fixes:
Fix multi-region iterator bugs on CRAM files.
Fixed multi-region iterator bug that caused some reads to be skipped incorrectly \
when reading BAM files.
Fixed synced_bcf_reader() bug when reading contigs multiple times.
Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary when \
removing samples.
Fixed bug where the VCF record ref length was calculated incorrectly if an INFO \
END tag was present. (71b00a)
Fixed warnings found when compiling with gcc 8.1.0.
sam_hdr_read() and sam_hdr_write() will now return an error code if passed a \
NULL file pointer, instead of crashing.
Fixed possible negative array look-up in sam_parse1() that somehow escaped \
previous fuzz testing.
Fixed bug where cram range queries could incorrectly report an error when using \
multiple threads.
Fixed very rare rANS normalisation bug that could cause an assertion failure \
when writing CRAM files.

Log message:
*: Move SUBST_STAGE from post-patch to pre-configure
Performing substitutions during post-patch breaks tools such as mkpatches,
making it very difficult to regenerate correct patches after making changes,
and often leading to substituted string replacements being committed.

Log message:
biology/htslib: import htslib-1.8
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.